Convert KEGG KO ids

Question

[yp19]

Hi all,

I just ran BlastKOALA and received my output which is basically a 2 column table with my protein IDs and their KO id.

prot_1      K22938

I would like to know how I can convert those KO ids to name & description. I can get the name and description by searching the KO ids one by one here: https://www.kegg.jp/kegg/

but I'd like an automatic way to do it as I have many. Is there some conversion table out there that I can use? or better, is there an option that we can select when submitting BlastKOALA that outputs KO id, name, description?

Thanks for your input.

Answer 1

[AK]

Hi yl2019,

If you want the name and definition only, you can fetch the table from http://rest.kegg.jp/list/ko. For example:

$ wget -O KO.txt "http://rest.kegg.jp/list/ko"
$ head -n5 KO.txt
ko:K00001   E1.1.1.1, adh; alcohol dehydrogenase [EC:1.1.1.1]
ko:K00002   AKR1A1, adh; alcohol dehydrogenase (NADP+) [EC:1.1.1.2]
ko:K00003   hom; homoserine dehydrogenase [EC:1.1.1.3]
ko:K00004   BDH, butB; (R,R)-butanediol dehydrogenase / meso-butanediol dehydrogenase / diacetyl reductase [EC:1.1.1.4 1.1.1.- 1.1.1.303]
ko:K00005   gldA; glycerol dehydrogenase [EC:1.1.1.6]

$ grep 'K22938' KO.txt
ko:K22938   SDCCAG3, ENTR1; serologically defined colon cancer antigen 3

In which the entry K22938 is with name: "SDCCAG3, ENTR1" and definition: "serologically defined colon cancer antigen 3".

[yp19]

That's awesome. Thanks so much!

Answer 2

[Elisabeth Gasteiger]

You could also use UniProt (in particular the IDmapping service at https://www.uniprot.org/uploadlists) to map your identifiers to UniProtKB and then restrict to a species (e.g. organism:9606) and possibly reviewed entries (reviewed:yes). The mapping results can be displayed in a table including gene gene and protein names.

This service can also be used programmatically.